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Crystal structure of ATAD2A bromodomain complexed with H3(1-21)K14Ac peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 278 2.0M Ammonium sulfate, 100mM Tris pH8.5.
Crystal Properties Matthews coefficient Solvent content 3.86 68.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.16 α = 90 b = 115.68 β = 90 c = 77.5 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 CCD ADSC QUANTUM 315r 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 57.84 99.9 0.2 0.084 0.992 6 6.7 13680
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 0.818 0.335 0.89 2.2 7 1790
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DAI 2.7 79.01 13654 681 99.7 0.2161 0.2149 0.2299 0.2404 0.2549 RANDOM 32.511
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.53 0.01 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_3_deg 14.56 r_dihedral_angle_4_deg 14.307 r_dihedral_angle_1_deg 4.533 r_mcangle_it 2.736 r_mcbond_it 1.707 r_mcbond_other 1.701 r_angle_refined_deg 1.215 r_angle_other_deg 1.045 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_3_deg 14.56 r_dihedral_angle_4_deg 14.307 r_dihedral_angle_1_deg 4.533 r_mcangle_it 2.736 r_mcbond_it 1.707 r_mcbond_other 1.701 r_angle_refined_deg 1.215 r_angle_other_deg 1.045 r_chiral_restr 0.123 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2201 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction